Chr9 Summary



# of exons in each CC

##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##   1.000   1.000   1.000   1.638   1.000  74.000



# of CC total: 14706
# of CC w/ one exon: 13545



# of CCs by # of exons



mean exon expr. by # of exons



median exon expr. by # of exons





Single exon CCs

## [1] TRUE



location on chr9



median vs. MAD expr. of single exon CCs



There were 254 unique UCSC genes that overlapped with 830 unique CCs. Total number of overlaps was 845.



We now add UCSC KnownGenes to above tracks plots. Note that these are not real transcripts, just the ‘union’ transcripts for each gene constructed by joining all reported isoforms. (note: need to specify fixed() <- TRUE for ucsc track since plot includes ideogram.)



Next, we focus on SPATA31A5 which overlapped with 39 single exon CCs.

## 
## uc004abu.4 uc004adx.4 
##         21         18





Two exon CCs



# of exons in each CC

## exon_cnts
##     1     2     3     4     5     6 
## 13545   467    81    49    47    48



# of exons/junctions in each CC

## ej_cnts
##     1     2     3     4     5     6 
## 13545   353   133    14    45     7



some CCs with 2 exons but no junctions

##  [1] "gene10047" "gene10054" "gene10064" "gene10097" "gene10135"
##  [6] "gene10150" "gene10190" "gene10195" "gene10198" "gene10241"
##            gIdx   gStart    gStop kind    start     stop
## 17956 gene10047 95349693 95349748    e 95349693 95349730
## 17957 gene10047 95349693 95349748    e 95349731 95349748




p16/p14 region



ucsc browser for chr9:21,960,000-22,090,000 ucsc





CC gene models



compare UCSC CDKN2A models vs. CCs in region



include nearby genes



most likely connected component was gene1791





Plotting exon expression (one CC)



equal width exons



adding annotations





PCA exon expression (one CC)



looking at clustering along the exons at p16



exon PCA decomposition (scores)



exon PCA decomposition (loadings)



look at clusters



scores by clusters



expression by clusters



looking at clusters with all exons having equal width, onlying looking at first 11 exons





Plotting junction coverage (one CC)



look at clusters



scores by clusters



expression by clusters



splice junction PCA decomposition (scores)





Graph-based view (one CC)





R Environment

Running Time

##    user  system elapsed 
##  71.199   2.063  73.750

Last Updated

## [1] "2014-11-04 00:44:40 EST"

Session Information

## R version 3.1.1 (2014-07-10)
## Platform: x86_64-apple-darwin13.3.0 (64-bit)
## 
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## attached base packages:
## [1] grid      parallel  stats     graphics  grDevices utils     datasets 
## [8] methods   base     
## 
## other attached packages:
##  [1] mvnmle_0.1-11                           
##  [2] igraph_0.7.1                            
##  [3] PTAk_1.2-9                              
##  [4] tensor_1.5                              
##  [5] org.Hs.eg.db_2.14.0                     
##  [6] RSQLite_1.0.0                           
##  [7] DBI_0.3.1                               
##  [8] TxDb.Hsapiens.UCSC.hg19.knownGene_2.14.0
##  [9] BSgenome.Hsapiens.UCSC.hg19_1.3.1000    
## [10] annotate_1.42.1                         
## [11] SplicingGraphs_1.4.1                    
## [12] Rgraphviz_2.8.1                         
## [13] graph_1.42.0                            
## [14] GenomicAlignments_1.0.6                 
## [15] BSgenome_1.32.0                         
## [16] Rsamtools_1.16.1                        
## [17] Biostrings_2.32.1                       
## [18] XVector_0.4.0                           
## [19] GenomicFeatures_1.16.3                  
## [20] AnnotationDbi_1.26.1                    
## [21] Biobase_2.24.0                          
## [22] GenomicRanges_1.16.4                    
## [23] GenomeInfoDb_1.0.2                      
## [24] IRanges_1.22.10                         
## [25] RColorBrewer_1.0-5                      
## [26] ggbio_1.12.10                           
## [27] BiocGenerics_0.10.0                     
## [28] ggplot2_1.0.0                           
## [29] rmarkdown_0.3.3                         
## 
## loaded via a namespace (and not attached):
##  [1] acepack_1.3-3.3          base64enc_0.1-2         
##  [3] BatchJobs_1.5            BBmisc_1.8              
##  [5] BiocParallel_0.6.1       biomaRt_2.20.0          
##  [7] biovizBase_1.12.3        bitops_1.0-6            
##  [9] brew_1.0-6               checkmate_1.5.0         
## [11] cluster_1.15.3           codetools_0.2-9         
## [13] colorspace_1.2-4         compiler_3.1.1          
## [15] dichromat_2.0-0          digest_0.6.4            
## [17] evaluate_0.5.5           fail_1.2                
## [19] foreach_1.4.2            foreign_0.8-61          
## [21] formatR_1.0              Formula_1.1-2           
## [23] gridExtra_0.9.1          gtable_0.1.2            
## [25] Hmisc_3.14-5             htmltools_0.2.6         
## [27] iterators_1.0.7          knitr_1.7               
## [29] labeling_0.3             lattice_0.20-29         
## [31] latticeExtra_0.6-26      MASS_7.3-35             
## [33] munsell_0.4.2            nnet_7.3-8              
## [35] plyr_1.8.1               proto_0.3-10            
## [37] Rcpp_0.11.3              RCurl_1.95-4.3          
## [39] reshape2_1.4             rpart_4.1-8             
## [41] rtracklayer_1.24.2       scales_0.2.4            
## [43] sendmailR_1.2-1          splines_3.1.1           
## [45] stats4_3.1.1             stringr_0.6.2           
## [47] survival_2.37-7          tools_3.1.1             
## [49] VariantAnnotation_1.10.5 XML_3.98-1.1            
## [51] xtable_1.7-4             yaml_2.1.13             
## [53] zlibbioc_1.10.0